GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Azospirillum brasilense Sp245

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS25635 AZOBR_RS25635 high-affinity branched-chain amino acid ABC transporter (permease protein) (fragment)

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__azobra:AZOBR_RS25635
          Length = 328

 Score =  190 bits (483), Expect = 4e-53
 Identities = 119/336 (35%), Positives = 186/336 (55%), Gaps = 48/336 (14%)

Query: 13  VALLV---LPLILQSFGNAWV-RIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGA 68
           +ALLV   LP +L  F   +  +IA+LAL+++LL+  +++V G AGLL LG+ AFY VGA
Sbjct: 7   LALLVFVGLPAVLAGFDRGYFYQIANLALIFILLSASMHLVTGVAGLLHLGHAAFYGVGA 66

Query: 69  YLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYL 128
           Y  AL+++                GL     + +P++ L+AA    ++  PT++L   Y 
Sbjct: 67  YTAALLSTKF--------------GL--GFTVTLPLSGLVAALIAFLVALPTMRLVSIYF 110

Query: 129 AIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTL 188
           A+ TL  G+++ + + N    V  T GP G+            + K LE+FGF ++    
Sbjct: 111 AVATLAIGQMLYLVMLNW---VEFTKGPNGI-----------IVTKGLELFGFSLSGRLA 156

Query: 189 YYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFG 248
            YY    +V + V+   RL  S  G A  +IRED+  A AMG++T  +K+ AF + A F 
Sbjct: 157 TYYTVATVVALCVLAIGRLSHSYYGNALRSIREDDQCADAMGVSTARLKMEAFTLSAFFA 216

Query: 249 GVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVA 308
           GV+G+++    G++SP  F   ES++I+AMVV+GG+G +PG ++GA+LL  LPE LR   
Sbjct: 217 GVAGSLWAHMTGYISPGDFKFSESILILAMVVVGGLGSLPGAVIGALLLILLPEGLR--- 273

Query: 309 GPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344
               A  D        R +++ L M + +LL P+GL
Sbjct: 274 ----AFGD-------FRNIMVGLVMFLSILLLPKGL 298



 Score = 24.3 bits (51), Expect = 0.005
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 7/48 (14%)

Query: 9   IIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLL 56
           +IGA+ L++LP  L++FG       D   + V L + L+I++   GLL
Sbjct: 259 VIGALLLILLPEGLRAFG-------DFRNIMVGLVMFLSILLLPKGLL 299


Lambda     K      H
   0.328    0.144    0.430 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 312
Number of extensions: 16
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 358
Length of database: 328
Length adjustment: 29
Effective length of query: 329
Effective length of database: 299
Effective search space:    98371
Effective search space used:    98371
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory